//
//  ClustalW.h
//  iBioCAD
//
//  Created by Orbitus on 10/22/07.
//  Copyright 2007 __MyCompanyName__. All rights reserved.
//

#import <Cocoa/Cocoa.h>
#import "iBioCAD_Controller.h"

@interface ClustalW : NSObject {

	IBOutlet iBioCAD_Controller *myController;

	IBOutlet NSButton *clustalButton;
	IBOutlet NSProgressIndicator *appRunningIndicator;
	IBOutlet NSArrayController *dnaArrayController;
	IBOutlet NSTextView*	clustalOutput;
	
	IBOutlet NSButton *onlyDendrogramFile;
	IBOutlet NSButton *useOldDendrogramFile;
	IBOutlet NSPathControl *dendrogramPath;
	IBOutlet NSPopUpButton *pwmatrix;
	IBOutlet NSPopUpButton *pwdnamatrix;
	IBOutlet NSPathControl *pairwiseDataFile;	
	IBOutlet NSPopUpButton *matrix;
	IBOutlet NSPopUpButton *dnamatrix;	
	IBOutlet NSPathControl *comparisonMatrixFile;	
	IBOutlet NSButton *slow;
	
	
	IBOutlet NSTextField *pwgapopen;
	IBOutlet NSTextField *pwgapextend;
	IBOutlet NSTextField *ktup;
	IBOutlet NSTextField *gapw;
	IBOutlet NSTextField *topDiags;
	IBOutlet NSTextField *window;
	IBOutlet NSButton *noPercent;

	IBOutlet NSTextField *gapOpen;
	IBOutlet NSTextField *gapExtend;
	IBOutlet NSButton *endGaps;
	IBOutlet NSTextField *gapDist;
	IBOutlet NSButton *norgap;
	
	IBOutlet NSTextField *hgapres;
	IBOutlet NSButton *nohgap;
	IBOutlet NSTextField *maxDiv;
	
	// ----------
	
	
	
	NSTask *myClustal;
	NSPipe *pipe;
	NSMutableArray *myArguments;
	
	NSBundle*	myBundle;
	NSString*	myAppPath;
	NSString*	myAppFolderPath;
	NSString*	myBinFolderPath;
	NSString*	myDataFolderPath;
	NSString*	myDesktopFolderPath;
	NSString*	clustalPath;
	
	NSManagedObjectContext	*managedObjectContext;
	NSManagedObjectModel	*managedObjectModel;
}
- (IBAction)Clustal:(id)sender;

@end
